Food allergy (FA) is an aberrant immune response triggered by the ingestion of a food antigen. Ovalbumin (OVA)-sensitized and challenged BALB/c mice were orally administered heat-killed (HK)-Lactobacillus paracasei JY56. In this work, HK-L. paracasei JY56 alleviated the FA-induced decrease in body weight and rectal temperature and reduced the allergy score. Serum analysis showed that HK-L. paracasei JY56 reduced the levels of specific antibodies (OVA-specific Immunoglobulin E (sIgE) and OVA-specific Immunoglobulin G (sIgG)) and allergic mediators (histamine and mast cell protease) in FA mice. In addition, HK-L. paracasei JY56 also could alleviate OVA-induced FA by suppressing T helper (Th)2 and Th17-type immune responses, which was evidenced by the regulation of splenic lymphocyte subpopulations and associated cytokine secretion. Moreover, jejunal histological analysis and intestinal barrier function related gene expression measurement were performed to verify the intestinal barrier repair of HK-L. paracasei JY56. Meanwhile, the TLR4/NF-κB inflammatory pathway activation was inhibited by HK-L. paracasei JY56 at gene and protein levels. Finally, HK-L. paracasei JY56 was performed to modulate the gut microbiota structure and increase the levels of short-chain fatty acids. In conclusion, HK-L. paracasei JY56 could alleviate OVA-induced FA in multiple ways, and this study provides a theoretical basis for the application of inactivated probiotics in functional foods for FA.